Chinese population linkage analysis single nucleotide polymorphism (SNP) marker sets and use method and application thereof

A linkage analysis, a Chinese technology, applied in the field of linkage analysis in genetics and genomics, can solve the problems of difficult product application and inability to meet the genetic analysis of Asian populations

Inactive Publication Date: 2011-07-13
BEIJING INST OF GENOMICS CHINESE ACAD OF SCI CHINA NAT CENT FOR BIOINFORMATION +1
View PDF0 Cites 19 Cited by
  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

One is that commercial markers in population design are based on the genetic background of Europeans, which cannot meet the ge

Method used

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
View more

Image

Smart Image Click on the blue labels to locate them in the text.
Viewing Examples
Smart Image
  • Chinese population linkage analysis single nucleotide polymorphism (SNP) marker sets and use method and application thereof
  • Chinese population linkage analysis single nucleotide polymorphism (SNP) marker sets and use method and application thereof
  • Chinese population linkage analysis single nucleotide polymorphism (SNP) marker sets and use method and application thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0037] Example 1. The method of using the SNP marker site:

[0038] Probe preparation: Custom synthesis of oligonucleotide probes for all 6001 SNP sites (Illumina typing system). The oligonucleotide probe is a nucleotide sequence containing the SNP site and its upstream and downstream tens of bp, and the SNP site contains two bases that are complementary to the dimorphic base of the SNP. Therefore, corresponding to one SNP site, there are two kinds of single nucleotide probes. Different nucleotide probe preparation companies have slight differences in the processing of probes. Usually, the synthetic oligonucleotide probes with SNP polymorphic sites are immobilized on tiny magnetic beads and attached to special silicon beads. In the microwell of the glass slide, or directly fixed on the slide, a large number of probes can be placed in a very small space, so as to achieve the high-throughput genotyping efficiency of the microchip.

[0039]Collection and storage of family sampl...

Embodiment 2

[0052] Example 2. Linkage Analysis Using Marker Locus Genotypes

[0053] Localization of pathogenic factors in two families with retinitis pigmentosa.

[0054] Experimental objects: two families as Figure 4 with Figure 5 shown. The first family was from Yongqing County, Hebei Province, including 77 individuals, 14 of whom were sick, and a total of 43 blood samples were taken, 36 of whom entered the experiment and linkage analysis; the second family was in Heze, Shandong, including 59 individuals, of whom 12 people were sick, and blood samples were taken from 23 people, 16 of whom participated in the experiment and analysis process. There was no consanguineous marriage in either family.

[0055] According to the characteristics of the families, the two RP families were determined to be autosomal dominant, and some family members were carriers of disease factors. RP showed incomplete penetrance in both families.

[0056] Preparation of sample DNA: As described in the meth...

Embodiment 3

[0074] Example 3. Effect Verification

[0075] After the disease gene candidate regions were obtained as in Examples 1 and 2, STR marker pairs were selected near the candidate regions to verify the localization results.

[0076]The STR markers D1S425 and D8S1771 were selected in the target region of chromosome 8 and chromosome 1 in family 1 and the experiment was completed. The linkage analysis software Mlink was used to analyze the STR data, and the LOD values ​​were 1.710 and 1.852 respectively; The two candidate regions selected nearby STR markers D14S258 and D14S68 with LOD values ​​of 3.160 and 2.600, respectively. Considering that the selectable STR loci cannot completely fall within the candidate chromosomal region and the heterozygosity of STR itself in the RP family, this result better verifies the linkage relationship between the candidate region and RP disease.

[0077] By searching the gene functions in the candidate region and literature reports, a gene Nrg1 rela...

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to view more

PUM

No PUM Login to view more

Abstract

The invention relates to Chinese population linkage analysis single nucleotide polymorphism (SNP) marker sets and a use method and application thereof. On the basis of hundreds of millions of Chinese Han population data results in the mass data of the International HapMap Project, medium-density and high-density SNP marker sets for linkage analysis are constructed and optimized, according to the statistical comparisons of multiple parameters such as the linkage disequilibrium, the polymorphism level, the typing success rate, the distribution position and density of genomes and the functional characteristic, and the multi-level selections and experimental verifications. The two marker sets separately contain 3000 and 6001 loci, wherein the 6001 loci contain the 3000 loci. The SNP sets aim at the Han genetic background in design, have high polymorphism in Chinese and can realize the aim of efficiently marking the Chinese family sample genomes. The selection of polymorphic loci is based on the neutral evolution principle, and all the loci are in a non-gene function region, thus the influence of evolution on the gene function can be avoided. Meanwhile, the characteristics that the marking loci have high typing detectability and can uniformly cover the whole genomes can ensure that the whole genomes can be screened completely and new pathogenic genes can be located and found. The two sets of SNP markers are used to customize probes or chips and perform whole-genome genotyping to family samples; and the typing data are used for linkage analysis, and the haplotyping and fine locating of the linkage candidate region are also adopted, thus the use method has more accurate locating result than the traditional method while the cost is lower and the speed is higher. The distribution and coverage of the 6001 SNP marker set in human chromosomes are shown in the appended drawings.

Description

Technical field: [0001] The invention relates to a set of SNP markers containing 3000 and 6001 medium and high density sets for linkage analysis, and belongs to the field of linkage analysis in genetics and genomics. These two sets of marker loci are completely based on the genetic background of Chinese people, and have many characteristics such as high polymorphism, uniform coverage of the whole genome, and high genotyping detection. It is suitable for genome-wide linkage analysis of the Chinese population, especially the Han population, and can achieve the purpose of efficiently locating the causative genes of the detected family genetic diseases. Background technique: [0002] In the study of gene mapping of complex diseases, genome-wide scans of research samples are often required to determine the location of the target gene on the chromosome. At present, there are two main methods, association analysis based on case-control samples and linkage analysis based on family ...

Claims

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to view more

Application Information

Patent Timeline
no application Login to view more
IPC IPC(8): C12Q1/68C12N15/11
Inventor 不公告发明人
Owner BEIJING INST OF GENOMICS CHINESE ACAD OF SCI CHINA NAT CENT FOR BIOINFORMATION
Who we serve
  • R&D Engineer
  • R&D Manager
  • IP Professional
Why Eureka
  • Industry Leading Data Capabilities
  • Powerful AI technology
  • Patent DNA Extraction
Social media
Try Eureka
PatSnap group products

Browse by: Latest US Patents, China's latest patents, Technical Efficacy Thesaurus, Application Domain, Technology Topic.

© 2024 PatSnap. All rights reserved.Legal|Privacy policy|Modern Slavery Act Transparency Statement|Sitemap